Sequence-specific detection of short-length DNA via template-dependent surface-hybridization events

OWL2: a molecular beacon-based nanostructure for highly selective detection of single-nucleotide variations in folded nucleic acids

Hybridization probes have been used in the detection of specific nucleic acids for the last 50 years. Despite the extensive efforts and the great significance, the challenges of the commonly used probes include (1) low selectivity in detecting single nucleotide variations (SNV) at low (e.g. room or 37 °C) temperatures; (2) low affinity in binding folded nucleic acids, and (3) the cost of fluorescent probes. Here we introduce a multicomponent hybridization probe, called OWL2 sensor, which addresses all three issues. The OWL2 sensor uses two analyte binding arms to tightly bind and unwind folded analytes, and two sequence-specific strands that bind both the analyte and a universal molecular beacon (UMB) probe to form fluorescent 'OWL' structure. The OWL2 sensor was able to differentiate single base mismatches in folded analytes in the temperature range of 5-38 °C. The design is cost-efficient since the same UMB probe can be used for detecting any analyte sequence.

Short DNA-catalyzed formation of quantum dot-DNA hydrogel for enzyme-free femtomolar specific DNA assay

Fast, sensitive, specific, and user-friendly DNA assay is a key technique for the next generation point-of-care molecular diagnosis. However, high-cost, time-consuming, and complicated enzyme-based DNA amplification step is essential to achieve high sensitivity. Herein, a short target DNA-catalyzed formation of quantum dot (QD)-DNA hydrogel is proposed as a new DNA assay platform satisfying the above requirements. A single-stranded target DNA catalyzes the opening cycle of DNA hairpin loops, which are quickly self-assembled with DNA-functionalized QDs to generate QD-DNA hydrogel. The three-dimensional hydrogel network allows efficient resonance energy transfer, dramatically lowering the limit of detection down to ~6 fM without enzymatic DNA amplification. The QD-DNA hydrogel also enables a rapid detection (1 h) with high specificity even for a single-base mismatch. The clinical applicability of the QD-DNA hydrogel is demonstrated for the Klebsiella pneumoniae carbapenemase gene, one of the key targets of drug-resistant pathogenic bacteria.

Single-Step Printable Hydrogel Microarray Integrating Long-Chain DNA for the Discriminative and Size-Specific Sensing of Nucleic Acids

A simple approach to fabricating hydrogel-based DNA microarrays is reported by physically entrapping the rolling circle amplification (RCA) product inside printable in situ gelling hydrazone cross-linked poly(oligoethylene glycol methacrylate) hydrogels. The hydrogel-printed RCA microarray facilitates improved RCA immobilization (>65% even after vigorous washing) and resistance to denaturation relative to RCA-only printed microarrays in addition to size-discriminative sensing of DNA probes (herein, 27 or fewer nucleotides) depending on the internal porosity of the hydrogel. Furthermore, the high number of sequence repeats in the concatemeric RCA product enables high-sensitivity detection of complementary DNA probes without the need for signal amplification, with signal/noise ratios of 10 or more achieved over a short 30 min assay time followed by minimal washing. The inherent antifouling properties of the hydrogel enable discriminative hybridization in complex biological samples, particularly for short (∼10 nt) oligonucleotides whose hybridization in other assays tends to be transient and of low affinity. The scalable manufacturability and efficient performance of these hydrogel-printed RCA microarrays thus offer potential for rapid, parallel, and inexpensive sensing of short DNA/RNA biomarkers and ligands, a critical current challenge in diagnostic and affinity screening assays.

A photocleavable and mass spectrometric DNA-peptide probe enables fast and specific enzyme-free detection of microRNA

MiRNAs are known to be involved in a series of diseases, including breast cancer, and they have the potential to serve as diagnostic/prognostic markers and therapeutic targets. A prerequisite for miRNAs to be applied in clinical practice is the quantitative profiling of their expression. However, the majority of current assays used in miRNA detection are highly enzyme-dependent. In this study, a novel enzyme-free assay was developed that relies on stacking hybridization and a photocleavable DNA-PL-peptide probe, which contains a reporter peptide (AVLGVDPFR), a photocleavable o-nitrobenzyl derivative linker and a detection DNA sequence that is complementary to a part of the target miRNA (e.g., miR-21, miR-125a or miR-200c). Stacking hybridization enabled the DNA-PL-peptide probe to capture DNA in a contiguous tandem arrangement to generate a long DNA single strand complementary to the target miRNA. Then, photolysis was initiated to rapidly release the reporter peptide, and the reporter peptide was ultimately monitored by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this experiment, the parameters linked with photorelease, binding, conjugation and hybridization were characterized. The results showed that the assay time was significantly shortened, and the detection specificity was improved. After validation of the assay, the target miRNA level was determined in human breast cells and tissue samples. The results demonstrated that photocleavable materials coupled with mass spectrometric detection have great potential in clinical practice.

Duplex microRNAs assay based on target-triggered universal reporter hybridization

In this paper, we designed and evaluated a duplex detection strategy for microRNAs (miRNAs) using universal probe-based target-triggered double hybridization and fluorescent microsphere-based assay system (xMAP array). In the absence of target miRNA, reporter DNA cannot hybridize stably with the immobilized capture DNA due to its low melting temperature. Only after adding target miRNA, can reporter probe hybridize with capture probe to form a stable three-component complex. This target-triggered stable hybridization makes this method possible for highly selective and sensitive detection of multiple miRNAs. We exemplified a quantitative detection of duplex miRNAs with a limit of detection of 40 pM. The xMAP array platform holds the potential of extending this approach to simultaneous detection of up to 100 miRNA targets. Considering the simplicity, rapidity and multiplexing, this work promised a potential detection of multiple miRNA biomarkers for early disease diagnosis and prognosis.

Probing cigarette smoke-induced DNA single-strand breaks and screening natural protective compounds by use of magnetic bead-based chemiluminescence

Magnetic bead (MB)-based chemiluminescence (CL) ELISA can be a sample-thrifty, time-saving tool for evaluation of cigarette smoke-induced DNA single-strand breaks (SSBs) with high specificity. This article describes a novel approach using immobilized oligonucleotide on MBs to determine cigarette smoke-induced DNA SSBs and screen some protective natural compounds. Typically, fluorescein-labeled DNA (FAM-DNA) was immobilized on the MBs and then oxidized by the smoke in the absence or presence of natural compounds, and a part of FAM-DNA was fragmented due to cigarette smoke-induced DNA SSB and then detached from MBs whereas other non-broken FAM-DNA still remained on MBs. Then, any broken FAM-DNA fragments, complex tobacco smoke matrix, and other stuff related with natural compounds were conveniently washed away by a magnetic force, and thus possible interfering substances were completely removed. Finally, those remaining non-broken FAM-DNA on MBs were reacted with HRP-labeled anti-fluorescein antibody and then detected by CL ELISA. CL signal was converted to molar concentrations of the FAM-DNA by interpolation from a pre-determined standard linear calibration curve. The level of DNA SSBs induced by cigarette smoke was thus calculated using the method. A library of 30 natural products was subsequently screened, and two among them were found to protect DNA from oxidative damage and thus may be promising compounds for the development of new drugs. The method developed will be useful for quantitative screening of drug genotoxicity in terms of induction of DNA SSBs. Graphical abstract ᅟ.

Fluorescence detection of telomerase activity in cancer cell extracts based on autonomous exonuclease III-assisted isothermal cycling signal amplification

Based on the extension reaction of a telomerase substrate (TS) primer in the presence of the telomerase, strand-displacement process to perform more stable longer duplex chain, and stepwise hydrolysis of mononucleotides from the blunt or the recessed 3'-hydroxyl termini of duplex DNA in the presence of Exonuclease III (Exo III), an amplified fluorescence detection of telomerase activity in the cancer cells was described in this manuscript. A fluorescence probe DNA, a quencher DNA, and a TS primer were mixed to construct a three-chain DNA structure and a two-chain DNA structure because the amount of the TS primer was less than the other two DNA. In the presence of the telomerase, the quencher DNA was replaced from the probe DNA and the telomerase activity could be determined with the fluorescence enhancement. The telomerase activity in HeLa extracts equivalent to 6-2000 cells was detected by this method. Moreover, the strategy was further proved by using telomerase extracted from Romas cells. With the multiple rounds of isothermal strand displacement and the hydrolysis process, constituted consecutive of signal amplification for the novel detection paradigm that allowed measuring of telomerase activity in crude cancer cell extracts confirmed the reliability and practicality of the protocol, which reveal this platform holds great promise in the biochemical assay for the telomerase activity in early diagnosis for cancers.

Invading stacking primer: A trigger for high-efficiency isothermal amplification reaction with superior selectivity for detecting microRNA variants

Searching for a strategy to enhance the efficiency of nucleic acid amplification and achieve exquisite discrimination of nucleic acids at the single-base level for biological detection has become an exciting research direction in recent years. Here, we have developed a simple and universal primer design strategy which produces a fascinating effect on isothermal strand displacement amplification (iSDA). We refer to the resultant primer as "invading stacking primer (IS-Primer)" which is based on contiguous stacking hybridization and toehold-mediated exchange reaction and function by merely changing the hybridization location of the primer. Using the IS-Primer, the sensitivity in detecting the target miR-21 is improved approximately five fold compared with the traditional iSDA reaction. It was further demonstrated that the IS-Primer acts as an invading strand to initiate branch migration which can increase the efficiency of the untwisting of the hairpin probe. This effect is equivalent to reducing the free energy of the stem, and the technique shows superior selectivity for single-base mismatches. By demonstrating the enhanced effect of the IS-Primer in the iSDA reaction, this work may provide a potentially new avenue for developing more sensitive and selective nucleic acids assays.

Rapid and Multiplexed MicroRNA Diagnostic Assay Using Quantum Dot-Based Förster Resonance Energy Transfer

The detection of next generation microRNA (miRNA) biomarkers has become a highly important aspect for clinical diagnostics. We use multiplexed Förster resonance energy transfer (FRET) between a luminescent Tb complex and three different semiconductor quantum dots (QDs) to sensitively detect three different miRNAs from a single 150 μL sample with ca. 1 nM (subpicomol) detection limits. The rapid and amplification-free mix-and-measure assay format is based on careful design of miRNA base pairing and stacking to selectively detect different miRNAs with very strong sequence homologies. Clinical applicability is demonstrated by sensitive multiplexed quantification of three miRNAs at low (2 to 10 nM) and varying concentrations in samples that contained up to 10% serum.

Chemiluminescent labels released from long spacer arm-functionalized magnetic particles: a novel strategy for ultrasensitive and highly selective detection of pathogen infections

Previously, the unique advantages provided by chemiluminescence (CL) and magnetic particles (MPs) have resulted in the development of many useful nucleic acid detection methods. CL is highly sensitive, but when applied to MPs, its intensity is limited by the inner filter-like effect arising from excess dark MPs. Herein, we describe a modified strategy whereby CL labels are released from MPs to eliminate this negative effect. This approach relies on (1) the magnetic capture of target molecules on long spacer arm-functionalized magnetic particles (LSA-MPs), (2) the conjugation of streptavidin-alkaline phosphatase (SA-AP) to biotinylated amplicons of target pathogens, (3) the release of CL labels (specifically, AP tags), and (4) the detection of the released labels. CL labels were released from LSA-MPs through LSA ultrasonication or DNA enzymolysis, which proved to be the superior method. In contrast to conventional MPs, LSA-MPs exhibited significantly improved CL detection, because of the introduction of LSA, which was made of water-soluble carboxymethylated β-1,3-glucan. Detection of hepatitis B virus with this technique revealed a low detection limit of 50 fM, high selectivity, and excellent reproducibility. Thus, this approach may hold great potential for early stage clinical diagnosis of infectious diseases.

A programmable Y-shaped junction scaffold-mediated modular and cascade amplification strategy for the one-step, isothermal and ultrasensitive detection of target DNA

A programmable Y-shaped junction probe-mediated modular and cascade amplification strategy was proposed for the one-pot, isothermal and ultrasensitive detection of target DNA.

Microchip capillary electrophoresis: quantum dots and paramagnetic particles for bacteria immunoseparation: rapid superparamagnetic-beads-based automated immunoseparation of Zn-Proteins from Staphylococcus aureus with nanogram yield

The emergence of drug-resistant bacteria and new or changing infectious pathogens is an important public health problem as well as a serious socioeconomic concern. Immunomagnetic separation-based methods create new possibilities for rapidly recognizing many of these pathogens. Nanomaterial-based techniques including fluorescent labeling by quantum dots as well as immunoextraction by magnetic particles are excellent tools for such purposes. Moreover, the combination with capillary electrophoresis in miniaturized microchip arrangement brings numerous benefits such as fast and rapid analysis, low sample consumption, very sensitive electrochemical and fluorescent detection, portable miniaturized instrumentation, and rapid and inexpensive device fabrication. Here the use of superparamagnetic particle-based fully automated instrumentation to isolate pathogen Staphylococcus aureus and its Zn(II)-containing proteins (Zn-proteins) is reported using a robotic pipetting system speeding up the sample preparation and enabling to analyze 48 real samples within 6 h. Cell lysis and Zn-protein extractions were obtained from a minimum of 100 cells with the sufficient yield for SDS-PAGE (several tens ng of proteins).

Rapid sub-attomole microRNA detection on a portable microfluidic chip

Microfluidic devices are an attractive choice for meeting the requirements of point-of-care microRNA detection. A method using a microfluidic device can drastically shorten the incubation time because the device conveys sample molecules right straight to the surface-immobilized probe DNAs by hydrodynamic force. In this review, we present an overview of a new method for rapid and sensitive microRNA detection from a small sample volume using a power-free microfluidic device driven by degassed poly-dimethylsiloxane (PDMS). Two key technologies for this detection method are summarized. One of the methods relies on the coaxial stacking effect of nucleic acids during sandwich hybridization. This effect is also efficient for stabilizing sandwich hybridization consisting of small DNA and microRNA. The other is the laminar flow-assisted dendritic amplification, which increases the fluorescent signal by supplying two amplification reagents from laminar streams to surface-bound molecules. Utilizing both technologies, microRNA detection is possible with a 0.5 pM detection limit from a 0.5 μL sample corresponding to 0.25 attomoles, with a detection time of 20 min. Since microRNAs are associated with various human diseases, future studies of these technologies might contribute to improved healthcare and may have both industrial and societal impacts.

Rapid and reliable microRNA detection by stacking hybridization on electrochemiluminescent chip system

MicroRNAs play pivotal roles in many fundamental aspects of life. Because microRNAs have the characteristics of small size, similar sequence, and low abundance, it is challenging to identify microRNAs rapidly and specifically with high sensitivity. Herein, we developed an electrochemiluminescent (ECL) chip system for microRNA detection based on base-stacking hybridization and magnetic microparticle enrichment technology. In the designed system, the integration of the microfluidic system with ECL detection made it easy to assemble the multiple assay steps and allowed the construction of a device that is convenient to carry. A limit of detection of 1fmol was achieved with this assay. The proposed direct optical microRNA detection technique demonstrated an acceptable sensitivity combined with the advantages of reliability and rapidity.

Hybridization chain reaction-based instantaneous derivatization technology for chemiluminescence detection of specific DNA sequences

We propose here a new amplifying strategy that uses hybridization chain reaction (HCR) to detect specific sequences of DNA, where stable DNA monomers assemble on the magnetic beads only upon exposure to a target DNA. Briefly, in the HCR process, two complementary stable species of hairpins coexist in solution until the introduction of initiator reporter strands triggers a cascade of hybridization events that yield nicked double helices analogous to alternating copolymers. Moreover, a "sandwich-type" detection strategy is employed in our design. Magnetic beads, which are functionalized with capture DNA, are reacted with the target, and sandwiched with the above nicked double helices. Then, chemiluminescence (CL) detection proceeds via an instantaneous derivatization reaction between a specific CL reagent, 3,4,5-trimethoxylphenylglyoxal (TMPG), and the guanine nucleotides within the target DNA, reporter strands and DNA monomers for the generation of light. Our results clearly show that the amplification detection of specific sequences of DNA achieves a better performance (e.g. wide linear response range, low detection limit, and high specificity) as compared to the traditional sandwich type (capture/target/reporter) assays. Upon modification, the approach presented could be extended to detect other types of targets. We believe that this simple technique is promising for improving medical diagnosis and treatment.

High affinity γPNA sandwich hybridization assay for rapid detection of short nucleic acid targets with single mismatch discrimination

Hybridization analysis of short DNA and RNA targets presents many challenges for detection. The commonly employed sandwich hybridization approach cannot be implemented for these short targets due to insufficient probe-target binding strengths for unmodified DNA probes. Here, we present a method capable of rapid and stable sandwich hybridization detection for 22 nucleotide DNA and RNA targets. Stable hybridization is achieved using an n-alkylated, polyethylene glycol γ-carbon modified peptide nucleic acid (γPNA) amphiphile. The γPNA's exceptionally high affinity enables stable hybridization of a second DNA-based probe to the remaining bases of the short target. Upon hybridization of both probes, an electrophoretic mobility shift is measured via interaction of the n-alkane modification on the γPNA with capillary electrophoresis running buffer containing nonionic surfactant micelles. We find that sandwich hybridization of both probes is stable under multiple binding configurations and demonstrate single base mismatch discrimination. The binding strength of both probes is also stabilized via coaxial stacking on adjacent hybridization to targets. We conclude with a discussion on the implementation of the proposed sandwich hybridization assay as a high-throughput microRNA detection method.

Microfluidic platform for isolating nucleic acid targets using sequence specific hybridization

The separation of target nucleic acid sequences from biological samples has emerged as a significant process in today's diagnostics and detection strategies. In addition to the possible clinical applications, the fundamental understanding of target and sequence specific hybridization on surface modified magnetic beads is of high value. In this paper, we describe a novel microfluidic platform that utilizes a mobile magnetic field in static microfluidic channels, where single stranded DNA (ssDNA) molecules are isolated via nucleic acid hybridization. We first established efficient isolation of biotinylated capture probe (BP) using streptavidin-coated magnetic beads. Subsequently, we investigated the hybridization of target ssDNA with BP bound to beads and explained these hybridization kinetics using a dual-species kinetic model. The number of hybridized target ssDNA molecules was determined to be about 6.5 times less than that of BP on the bead surface, due to steric hindrance effects. The hybridization of target ssDNA with non-complementary BP bound to bead was also examined, and non-specific hybridization was found to be insignificant. Finally, we demonstrated highly efficient capture and isolation of target ssDNA in the presence of non-target ssDNA, where as low as 1% target ssDNA can be detected from mixture. The microfluidic method described in this paper is significantly relevant and is broadly applicable, especially towards point-of-care biological diagnostic platforms that require binding and separation of known target biomolecules, such as RNA, ssDNA, or protein.

Rapid and sensitive microRNA detection with laminar flow-assisted dendritic amplification on power-free microfluidic chip

Detection of microRNAs, small noncoding single-stranded RNAs, is one of the key topics in the new generation of cancer research because cancer in the human body can be detected or even classified by microRNA detection. This report shows rapid and sensitive microRNA detection using a power-free microfluidic device, which is driven by degassed poly(dimethylsiloxane), thus eliminating the need for an external power supply. MicroRNA is detected by sandwich hybridization, and the signal is amplified by laminar flow-assisted dendritic amplification. This method allows us to detect microRNA of specific sequences at a limit of detection of 0.5 pM from a 0.5 µL sample solution with a detection time of 20 min. Together with the advantages of self-reliance of this device, this method might contribute substantially to future point-of-care early-stage cancer diagnosis.

Transglutaminase-mediated in situ hybridization (TransISH) system: a new methodology for simplified mRNA detection

Detection and localization of specific DNA or RNA sequences in cells and tissues are of great importance for biological research, diagnosis, and environmental monitoring. However, the most common procedure for in situ hybridization employs laborious immunostaining techniques. In the present study, we report proof-of-concept for a new RNA-enzyme conjugated probe for the detection of mRNA on tissue sections with a simple procedure. An RNA probe modified with a specific dipeptide substrate of transglutaminase was prepared. Alkaline phosphatase was then covalently and site-specifically combined to the dipeptide-labeled RNA using microbial transglutaminase. The new RNA probe labeled with alkaline phosphatase was validated by in situ hybridization (ISH) and proved to be a sensitive and sequence specific probe for mRNA detection in tissues. The new transglutaminase-mediated ISH (TransISH) strategy is free from antigen-antibody reaction, leads to one-step signal amplification after hybridization, and thus will be widely applicable for highly sensitive nucleic acid detection.

Signal-on electrochemical Y or junction probe detection of nucleic acid

A methylene-blue (MB)-labeled molecular beacon junction probe allows for a signal-on electrochemical detection of nucleic acids via target recycling using endonucleases. Electron transfer is reduced when the MB is intercalated in the stem of the molecular beacon, but then electron transfer from MB to a gold electrode is enhanced upon cleavage of the junction probe due to increased probability of MB approaching the electrode when attached to the more flexible ssDNA.

Quantitative experimental determination of primer-dimer formation risk by free-solution conjugate electrophoresis

DNA barcodes are short, unique ssDNA primers that "mark" individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer-barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer-dimer cases comprised two 30-mer primers, one of which was covalently conjugated to a lab-made, chemically synthesized poly-N-methoxyethylglycine drag-tag, which reduced electrophoretic mobility of ssDNA to distinguish it from ds primer-dimers. The drag-tags also provided a shift in mobility for the dsDNA species, which allowed us to quantitate primer-dimer formation. In the experimental studies, pairs of oligonucleotide primer barcodes with fully or partially complementary sequences were annealed, and then separated by free-solution conjugate CE at different temperatures, to assess effects on primer-dimer formation. When less than 30 out of 30 base-pairs were bonded, dimerization was inversely correlated to temperature. Dimerization occurred when more than 15 consecutive base-pairs formed, yet non-consecutive base-pairs did not create stable dimers even when 20 out of 30 possible base-pairs bonded. The use of free-solution electrophoresis in combination with a peptoid drag-tag and different fluorophores enabled precise separation of short DNA fragments to establish a new mobility shift assay for detection of primer-dimer formation.

Turn-on aptameric system for simple and selective detection of protein via base stacking-dependent DNA hybridization event

Base stacking is employed in an entirely new type of sensing platform for the simple and robust detection of protein. Only in the presence of protein, the aptamer DNA can hybridize stably with the capture DNA to form a stem-loop structure due to the enhancement of base stacking. This leads to a strong chemiluminescence emission for simple protein detection. With the use of a platelet-derived growth factor as a model, a fM detection limit was obtained with a dynamic range that spanned 4 orders of magnitude. Upon modification, the approach presented herein was also extended to detect other types of targets including Hg(2+) ion and adenosine and also other types of labels such as fluorescence nanogold. We believe such advancements will represent a significant step toward improved diagnostics and more personalized medical treatment and environmental monitoring.